It looks like the front already has a bit of framing started..? I would finish framing in the front with treated lumber and frame it in for a "people" door as tall as it will allow. Just cover the front of your finished framing with OSB or plywood, and paint that (to weather proof it) or put siding over that. You could also use T1-11 for the front over your studs that you add in and call it good without the plywood... but I'd probably use plywood under it anyway. I would just open that each morning to let them out in the run. I would attach the run to the front, as that makes the most sense. I agree with the vent on the top. Have you seen those spinner vents that are on top of homes? I think it would be pretty easy to install one of those. They are in the back of Lowes-- where all siding and roofing is. You'll probably just need one of them, the entire structure doesn't look too big. As for the holes in the bottom-- I'd get a roll of the short hardware cloth and screw it in along the bottom, or as someone else suggested, pour cement along the bottom. I think it would be really easy to convert! This is a GREAT idea!! 
